Merge pull request #5692 from RosettaCommons/roccomoretti/update_cmake_build Update CMake build Don't die if an only-with-extras external library isn't present on disk. (This fixes an issue I'm seeing on my machine with the bcl external library.)

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• integration.mpi 「2」

Merge pull request #5681 from RosettaCommons/guangfeng/galiganddock_update2 GALigandDock update

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• mac.clang.static.release.binary

Merge pull request #5668 from RosettaCommons/vmullig/fix_t900_distributed Fix the T900_distributed PyRosetta test Tasks: - [x] Removing thread index from T900 test. - [x] Confirm that this does fix the Linux PyRosetta tests.

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• integration.mpi 「1」
• mac.clang.static.release.binary

Merge pull request #5641 from RosettaCommons/brownbp1/bcl_submodule_updates_10-2021 Brownbp1/bcl submodule updates 10 2021

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• mac.clang.python27.release.PyRosetta4.Debug
• mac.clang.python36.release.PyRosetta4.Debug
• mac.clang.python37.release.PyRosetta4.Debug
• mac.clang.python38.release.PyRosetta4.Debug
• mac.clang.python39.release.PyRosetta4.Debug
• mac.clang.python27.release.PyRosetta4.MinSizeRel
• mac.clang.python36.release.PyRosetta4.MinSizeRel
• mac.clang.python37.release.PyRosetta4.MinSizeRel
• mac.clang.python38.release.PyRosetta4.MinSizeRel
• mac.clang.python39.release.PyRosetta4.MinSizeRel
• mac.clang.python27.release.PyRosetta4.Release
• mac.clang.python36.release.PyRosetta4.Release
• mac.clang.python37.release.PyRosetta4.Release
• mac.clang.python38.release.PyRosetta4.Release
• mac.clang.python39.release.PyRosetta4.Release
• mac.clang.cxx11thread.serialization.python36.release.PyRosetta4.conda.Release
• mac.clang.cxx11thread.serialization.python37.release.PyRosetta4.conda.Release
• mac.clang.cxx11thread.serialization.python38.release.PyRosetta4.conda.Release
• mac.clang.cxx11thread.serialization.python39.release.PyRosetta4.conda.Release
• mac.clang.static.release.binary

Merge pull request #5629 from RosettaCommons/update_Mcluster_9-30-21 updating ROSIE stabilize-cluster script

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• mac.clang.python27.release.PyRosetta4.Release
• mac.clang.cxx11thread.serialization.python36.release.PyRosetta4.conda.Release
• mac.clang.static.release.binary

Merge pull request #5607 from CyrusBiotechnology/forcommons/hybridize_fix_disulf HybridizeProtocol: expose disulf_file_ internal HybridizeProtocol has two constructors. The default constructor assumes data will come in via XML, and DOES check the value of the fix_disulf flag, storing it into an internal string disulf_file_ for later use. The argumented constructor sets class internals via either the arguments or hardcoded defaults and does NOT check the options system - in fact the code is there, commented out. Cyrus was bitten by this difference. In our fork I am unifying their behavior, but I am uninterested in taking responsibility for making that type of default change globally. (If it were to be properly fixed, HybridizeProtocol should just use a different flag entirely for the purpose; as it is the C++ code in HybridizeProtocol does writing TO the option system to disable this flag during template read-in, because the flag is active at PDB read in time and causes templates to be misread when present...it's, uh, highly nonstandard). Here I expose disulf_file_ via a standard getter/setter and offer a unit tests that checks A) getting and setting work, and B) that the current constructor behaviors are maintained. I'm fine if RosettaCommons chooses to change the constructor behaviors to match each other in a subsequent PR (I will be doing so in our fork). I fixed the const & ness of the argumented ctor as a side effect; it made writing the unit test simpler because you can't pass a const string to a nonconst ref argument. TY sergey for kicking windows tests and Rocco for prompt review

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• integration.mpi 「2」
• mac.clang.static.release.binary

Merge pull request #5589 from RosettaCommons/weitzner/remove-inline-to-fix-pyro Remove `inline` keyword from `RNA_CoarseDistEnergy::deriv_atom_pair` …

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• integration.mpi 「1」
• mac.clang.static.release.binary

Merge pull request #5560 from RosettaCommons/roccomoretti/EnergyMap_array Convert EnergyMap to use a std::array. This is based off of PR #5556, and the hope is that the std::array will get around the GCC 11 errors that are seen with the copy constructor/assignment operator. (Mostly because we can defer the copy/assignment operations to the std::array versions.) This PR also removes the -fno-builtin flag from the GCC 11 compilation, which was previously added in PR #5552 as a workaround for the issue that this PR fixes.

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• integration.mpi 「2」
• mac.clang.static.release.binary

Merge pull request #5555 from RosettaCommons/vmullig/update_scripts Update the rosetta_scripts_scripst repo submodule to point to the latest master.

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• mac.clang.static.release.binary

Merge pull request #5541 from RosettaCommons/vmullig/fix_unused_using_decls Removing unused "using" declarations that clang-tidy was complaining about. This should fix the clang-tidy tests.

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• integration.mpi 「1」
• mac.clang.static.release.binary

Merge pull request #5045 from RosettaCommons/bcov/ApproxReview A few changes to approximate_buried_ for paper

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• linux.gcc.static.release.binary
• mac.clang.static.release.binary

dock pdb into density app (#5053) This is one of the apps I've made as part of my thesis project. it's purpose is to dock a pdb file, or ensemble of pdb files, into density and report back the ones that best fit the density currently i've called it dgdp for density guided domain placement, but that's sort of a strange name. maybe I'll just take over frank's pilot apps name (dock_pdb_into_density) It unfortunately overlaps with the DockIntoDensityMover a lot, but its differences are: it can be parallelized much more (which is necessary when docking large poses into density, otherwise one pdb can take 1+ days). there are important differences in the ways clustering is performed things are clustered not at the "point level" but rather over all points different mapresolutions are used during different stages to obtain more accurate density scoring. there is native checking implemented for multiple natives (ie multiple copies of the same chain in the complex) it also comes with a python script that manages the job distribution on a Slurm cluster (although I will add an option to run it locally) add documentation test script add some integration tests review the code and see what crazy things I was doing 4 years ago can confirm it's crazy change fragment docker name to dockfragmentmover

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• mac.clang.cxx11thread.serialization.python39.release.PyRosetta4.conda.Release 「52」
• mac.clang.static.release.binary

updating PyRosetta.notebooks to its latests master to fix notebooks tests

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• integration.mpi 「5」
• linux.gcc.unit 「5」

Merge pull request #5477 from RosettaCommons/revert-5476-revert-5468-woodsh17/mp_cart_ddg Revert "Revert "Add membrane option for cartesian_ddg""

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Merge pull request #4820 from RosettaCommons/JWLabonte/sugars/database2 Carbohydates: adding methylated sugars to the database This merge will add O-methylated sugars into the Rosetta database. (This merge integrates work started by former student @qjia73 and was expanded by @jonpliu .) Appropriate nomenclature will be added in PR #4793.

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Merge pull request #5456 from RosettaCommons/dimaio/masked_spharm_matcher Dimaio/masked spharm matcher

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